SMTL ID : 9ca9.1

Cryo-EM structure of the human SRCAP complex in the unbound state (composite structure)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-3-3-mer

Ligands

1 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 19 residues within 4Å: Chain C: G.9, A.10, Y.11, N.12, K.14, G.151, Y.152, S.153, F.154, G.177, N.203, K.206, E.207, G.321, G.322, L.325, F.326, I.356 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:A.10, C:Y.11, C:N.12, C:Y.152, C:S.153, C:N.203, C:N.203, C:K.206, C:E.207, C:G.322 Salt bridges: C:K.14, C:K.14 pi-Stacking: C:F.326

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 1 residues within 4Å: Ligands: AGS.1 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain F: T.84, D.299 Chain G: E.320, R.357 Ligands: ADP.6 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.84 MG.10: 3 residues within 4Å: Chain H: T.84 Chain I: R.357 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.84 MG.13: 5 residues within 4Å: Chain E: R.357 Chain J: T.84, D.299, E.300 Ligands: ADP.12 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.84

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain D: C.128, C.131, H.144, C.149 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.128, D:C.131, D:H.144, D:C.149 ZN.4: 4 residues within 4Å: Chain D: C.117, C.120, C.136, C.140 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.117, D:C.120, D:C.136, D:C.140

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 21 residues within 4Å: Chain E: S.17, H.18, H.20, G.38, L.39, V.40, G.41, P.71, P.72, G.73, T.74, G.75, K.76, T.77, A.78, Y.366, I.374, R.404 Chain F: R.314, E.317, R.353 22 PLIP interactions: 18 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:S.17, E:H.18, E:V.40, E:G.41, E:G.73, E:T.74, E:T.74, E:G.75, E:K.76, E:T.77, E:T.77, E:A.78, E:Y.366, E:Y.366, F:R.353, F:R.353 Salt bridges: E:H.18, E:K.76, E:R.404, E:R.404, F:R.314, F:R.314 ADP.6: 22 residues within 4Å: Chain F: A.24, H.25, H.27, I.28, G.45, M.46, V.47, Q.49, P.79, G.80, T.81, G.82, K.83, T.84, A.85, Y.362, I.370, L.399, R.400, I.403 Chain G: R.357 Ligands: MG.7 15 PLIP interactions: 14 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:H.25, F:V.47, F:G.80, F:T.81, F:T.81, F:G.82, F:K.83, F:T.84, F:A.85, F:Y.362, G:R.357 Salt bridges: F:H.25, F:K.83, F:R.400, F:R.400 ADP.8: 18 residues within 4Å: Chain G: S.17, H.18, H.20, G.38, L.39, V.40, P.72, G.73, T.74, G.75, K.76, T.77, A.78, Y.366, I.374, R.404 Chain H: R.314, R.353 17 PLIP interactions: 2 interactions with chain H, 15 interactions with chain G Hydrogen bonds: H:R.353, G:H.18, G:V.40, G:G.73, G:T.74, G:T.74, G:G.75, G:K.76, G:T.77, G:A.78, G:Y.366, G:Y.366 Salt bridges: H:R.314, G:H.18, G:K.76, G:R.404, G:R.404 ADP.9: 18 residues within 4Å: Chain H: A.24, H.25, H.27, G.45, M.46, V.47, P.79, G.80, T.81, G.82, K.83, T.84, A.85, Y.362, I.370, L.399, R.400 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:A.24, H:V.47, H:G.80, H:T.81, H:G.82, H:K.83, H:T.84, H:A.85, H:Y.362, H:Y.362 Salt bridges: H:H.25, H:K.83, H:R.400, H:R.400 ADP.11: 18 residues within 4Å: Chain I: S.17, H.18, H.20, G.38, L.39, V.40, P.71, G.73, T.74, G.75, K.76, T.77, A.78, Y.366, I.374, R.404 Chain J: R.314, R.353 20 PLIP interactions: 16 interactions with chain I, 4 interactions with chain J Hydrogen bonds: I:H.18, I:V.40, I:G.73, I:T.74, I:T.74, I:G.75, I:K.76, I:T.77, I:T.77, I:A.78, I:Y.366, I:Y.366, J:R.314, J:E.317, J:R.353 Salt bridges: I:H.18, I:K.76, I:R.404, I:R.404, J:R.314 ADP.12: 22 residues within 4Å: Chain E: R.357 Chain J: A.24, H.25, H.27, I.28, G.45, M.46, V.47, Q.78, P.79, G.80, T.81, G.82, K.83, T.84, A.85, Y.362, I.370, L.399, R.400, I.403 Ligands: MG.13 17 PLIP interactions: 16 interactions with chain J, 1 interactions with chain E Hydrogen bonds: J:H.25, J:V.47, J:Q.78, J:G.80, J:T.81, J:G.82, J:K.83, J:T.84, J:T.84, J:A.85, J:Y.362, J:Y.362, E:R.357 Salt bridges: J:H.25, J:K.83, J:R.400, J:R.400

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, G. et al., Structural divergence of H2A.Z-associated human chromatin remodelers SRCAP and TIP60. To Be Published

Release Date

2025-06-18

Peptides

Helicase SRCAP: A
Vacuolar protein sorting-associated protein 72 homolog: B
Actin-related protein 6: C
Zinc finger HIT domain-containing protein 1: D
RuvB-like 1: EGI
RuvB-like 2: FHJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

G
G

I
I

F
F

H
H

J
J

Helicase SRCAP

Vacuolar protein sorting-associated protein 72 homolog

Actin-related protein 6

Zinc finger HIT domain-containing protein 1

RuvB-like 1

RuvB-like 2

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